A5088354343- Cellular Mechanics and Interactions
- Single-cell and spatial transcriptomics
- Gene Regulatory Network Analysis
- RNA Research and Splicing
- Cell Image Analysis Techniques
- Microbial Community Ecology and Physiology
- Evolution and Genetic Dynamics
- Hippo pathway signaling and YAP/TAZ
- Genomics and Phylogenetic Studies
- 3D Printing in Biomedical Research
- Microtubule and mitosis dynamics
- Developmental Biology and Gene Regulation
- Fluid Dynamics and Heat Transfer
- Morphological variations and asymmetry
- Microfluidic and Bio-sensing Technologies
- Gene expression and cancer classification
- Plant Surface Properties and Treatments
- Force Microscopy Techniques and Applications
- Neurobiology and Insect Physiology Research
- Biocrusts and Microbial Ecology
- Micro and Nano Robotics
- Genetics, Aging, and Longevity in Model Organisms
- Genomics and Chromatin Dynamics
- Cancer-related molecular mechanisms research
- Advanced Materials and Mechanics
Northwestern University
2017-2024
Hôpital Sahloul
2024
Quantitative BioSciences
2020-2024
Cold Spring Harbor Laboratory
2024
Applied Mathematics (United States)
2017-2018
University of California, Santa Barbara
2011-2014
Harvard University
2009-2012
Kavli Institute for Particle Astrophysics and Cosmology
2011
Orthopaedic Research Group
2011
A high velocity impact between a liquid droplet and solid surface produces splash. Classical work traced the origin of splash to thin sheet fluid ejected near point. Mechanisms formation have heretofore relied on initial contact surface. We demonstrate that, neglecting intermolecular forces solid, does not instead spreads very air film. The interface develops curvature emits capillary waves.
A high-velocity (≈1 ms −1 ) impact between a liquid droplet mm) and solid surface produces splash. Classical observations traced the origin of this splash to thin sheet fluid ejected near point, though mechanical mechanism leading is not known. Mechanisms formation have heretofore relied on initial contact surface. In paper, we theoretically numerically study events within time scale about 1 μs over which coupled dynamics gas becomes important. The initially tries substrate by either...
During epithelial morphogenesis, cell contacts (junctions) are constantly remodeled by mechanical forces that work against adhesive forces. E-cadherin complexes play a pivotal role in this process providing persistent adhesion and transmitting tension. In context, it is unclear how affect junction dynamics. Drosophila embryo axis elongation, Myosin-II activity the apico-medial junctional cortex generates to drive remodeling. Here we report ratio between Vinculin intensities acts as...
Gene expression dynamics provide directional information for trajectory inference from single-cell RNA sequencing data. Traditional approaches compute velocity using strict modeling assumptions about transcription and splicing of RNA. This can fail in scenarios where multiple lineages have distinct gene or rates are time dependent. We present "LatentVelo," an approach to a low-dimensional representation with deep learning. LatentVelo embeds cells into latent space variational autoencoder...
Organismal development is a complex process, involving vast number of molecular constituents interacting on multiple spatio-temporal scales in the formation intricate body structures. Despite this complexity, remarkably reproducible and displays tolerance to both genetic environmental perturbations. This robustness implies existence hidden simplicities developmental programs. Here, using Drosophila wing as model system, we develop new quantitative strategy that enables robust description...
Pattern formation of biological structures involves the arrangement different types cells in an ordered spatial configuration. In this study, we investigate mechanism patterning Drosophila eye epithelium into a precise triangular grid photoreceptor clusters called ommatidia. Previous studies had led to long-standing biochemical model whereby reaction-diffusion process is templated by recently formed ommatidia propagate molecular prepattern across eye. Here, find that templating instead,...
Single-cell "omics"-based measurements are often high dimensional so that dimensionality reduction (DR) algorithms necessary for data visualization and analysis. The lack of methods separating signal from noise in DR outputs has limited their utility generating data-driven discoveries single-cell data. In this work we present EMBEDR, which assesses the output any algorithm to distinguish evidence structure algorithm-induced outputs. We apply EMBEDR DR-generated representations omics several...
Inspired by Waddington's illustration of an epigenetic landscape, cell-fate transitions have been envisioned as bifurcating dynamical systems, wherein exogenous signaling dynamics couple to a cell's enormously complex and transcriptional machinery, elicit qualitative in the collective state. Single-cell RNA sequencing (scRNA-seq), which measures distributions possible states large populations differentiating cells, provides alternate view, development is marked variations myriad genes. Here,...
Describing morphogenesis generally consists in aggregating the multiple high resolution spatiotemporal processes involved into reproducible low dimensional morphological consistent across individuals of same species or group. In order to achieve this goal, biologists often have submit movies issued from live imaging developing embryos either a qualitative analysis basic statistical analysis. These approaches, however, present noticeable drawbacks, as they can be time consuming, hence unfit...
We consider the sticking of a fluid-immersed colloidal particle with substrate coated by polymeric tethers, model for soft, wet adhesion in many natural and artificial systems. Our theory accounts kinetics binding, elasticity hydrodynamics fluid drainage between colloid substrate, characterized three dimensionless parameters: ratio viscous time to elastic thermal energies, size relative height polymer brush. For typical experimental parameters discrete families we find that proceeds via...
Significance Morphogenesis is a biological process that generates the physical form and structure of multicellular organisms. Although many genes controlling morphogenesis are known, little understood mechanisms define tissue shape size. Prominent among these contact signaling between cells mediated by two cell adhesion-type proteins Dachsous Fat, which regulate division in response to spatially graded distribution morphogens, factors governing patterning growth. Here, based on known...
During cell division, precise and regulated distribution of cellular material between daughter cells is a critical step governed by complex biochemical biophysical mechanisms. To achieve this, membraneless organelles condensates often require complete disassembly during mitosis. The principles governing the remain poorly understood. Here, we used physical biology approach to study how properties nucleolus, prominent nuclear organelle in eukaryotic cells, change mitosis across different...
ABSTRACT The field of developmental biology has declined in prominence recent decades, with off-shoots from the becoming more fashionable and highly funded. This created inequity discovery opportunity, partly due to perception that is antiquated or not cutting edge. A ‘think tank’ scientists multiple biology-related disciplines came together define specific challenges may have inhibited innovation, provide tangible solutions some issues facing biology. community suggestions include a call...
Ratcheting surfaces are a common motif in nature and appear plant awns grasses. They known to proffer selective advantages for seed dispersion burial. In two simple model experiments, we show that these anisotropically toothed naturally serve as motion rectifiers generically move unidirectional manner, when subjected temporally spatially symmetric excitations of various origins. Using combination theory experiment, linear relationship between awn length ratchet efficiency holds under...
Previous work has demonstrated that combining mechanical vibration with magnetic interactions can result in the self-assembly of complex structures, albeit at low yield. Here we introduce a system where yield self-assembled structures is quantitatively predicted by theoretical analysis. Millimeter-sized blocks, designed to form chains as their minimal energy state, are placed turbulent fluid flow. The distribution chain lengths consistent predictions, showing length coincides monomers or...
Sensory neuron numbers and positions are precisely organized to accurately map environmental signals in the brain. This precision emerges from biochemical processes within between cells that inherently stochastic. We investigated impact of stochastic gene expression on pattern formation, focusing senseless (sens), a key determinant sensory fate Drosophila. Perturbing microRNA regulation or genomic location sens produced distinct noise signatures. Noise was greatly enhanced when both alleles...
Morphogen signaling contributes to the patterned spatiotemporal expression of genes during development. One mode regulation signaling-responsive is at level transcription. Single-cell quantitative studies transcription have revealed that occurs intermittently, in bursts. Although effects many gene regulatory mechanisms on transcriptional bursting been studied, it remains unclear how morphogen gradients affect this dynamic property downstream genes. Here we adapted single molecule...